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How about mat[,order(colnames(mat))]?
Best,
Jim
carol white wrote:
> Hello,
> How to sort a matrix based on its column names and preserving the
identical column names.
>
> when I use mat [, sort(colnames(mat))], sort changes all column
names to unique ones. for ex, if the name of 2 columns is col, the
2nd will be changed to col.1 whereas I want to keep the col name for
the two columns
>
> col col -> col col.1
>
> thanks
>
>
> ---------------------------------
> Park yourself in front of a world of choices in alternative
vehicles.
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
0
Entering edit mode
Oh, wait. I didn't read the part about the repeated column names. I
don't think you can resort without ending up with unique column names.
Sorry for the noise...
carol white wrote:
> Hello,
> How to sort a matrix based on its column names and preserving the
identical column names.
>
> when I use mat [, sort(colnames(mat))], sort changes all column
names to unique ones. for ex, if the name of 2 columns is col, the
2nd will be changed to col.1 whereas I want to keep the col name for
the two columns
>
> col col -> col col.1
>
> thanks
>
>
> ---------------------------------
> Park yourself in front of a world of choices in alternative
vehicles.
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
0
Entering edit mode
Joern Toedling
▴
730
@joern-toedling-1244
Last seen 10.2 years ago
Hi Carol,
despite the fact that it is certainly preferable to have unique column
names and this can prevent all sorts of hard-to-debug confusion later
on,
I think there is something missing from your example code.
If you really only have a matrix and only do some resorting of the
colums you will definitely keep the original colum names,
check this example:
> A = matrix(rnorm(6),nrow=2)
> colnames(A)<-c("bla","bal","bla")
> A
bla bal bla
[1,] -1.1283559 -0.5672175 -1.135924
[2,] -0.8160838 -0.7441979 1.395936
> (A[,sort(colnames(A))])
bal bla bla
[1,] -0.5672175 -1.1283559 -1.1283559
[2,] -0.7441979 -0.8160838 -0.8160838
Actually, you will notice that the second and third column are
identical, since after the sorting the first occurrence of the column
name is taken from A.
To prevent that you should not index the matrix using a character
vector
but the numeric indices (or use unique column names):
> (A[,order(colnames(A))])
bal bla bla
[1,] -0.5672175 -1.1283559 -1.135924
[2,] -0.7441979 -0.8160838 1.395936
Renaming of column names, however, only happens when you convert the
matrix into a data.frame:
> data.frame(A)
bla bal bla.1
1 -1.1283559 -0.5672175 -1.135924
2 -0.8160838 -0.7441979 1.395936
and this renaming can be prevented by setting the argument
check.names=FALSE
> data.frame(A, check.names=FALSE)
bla bal bla
1 -1.1283559 -0.5672175 -1.135924
2 -0.8160838 -0.7441979 1.395936
Best regards,
Joern
carol white wrote:
> Hello,
> How to sort a matrix based on its column names and preserving the
identical column names.
>
> when I use mat [, sort(colnames(mat))], sort changes all column
names to unique ones. for ex, if the name of 2 columns is col, the
2nd will be changed to col.1 whereas I want to keep the col name for
the two columns
>
> col col -> col col.1
>
> thanks
>
>
> ---------------------------------
> Park yourself in front of a world of choices in alternative
vehicles.
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
0
Entering edit mode
Oleg Sklyar
▴
260
@oleg-sklyar-1882
Last seen 10.2 years ago
mat[, order(colnames(mat))]
order provides indexes of sorted elements without affecting their
names.
Sort works in your case half ways only because you are sorting
characters, and columns can be identified by characters, otherwise it
is
wrong.
Here is the working example:
> x<-c("col","abc","def","abc","col")
> a<-matrix(runif(25),ncol=5,nrow=5)
> colnames(a) <- x
> a
col abc def abc col
[1,] 0.9815985 0.65855865 0.9982046 0.07781167 0.3228944
[2,] 0.5970836 0.19195563 0.9082061 0.80489513 0.9190933
[3,] 0.8147790 0.13499074 0.9431437 0.41154237 0.6487952
[4,] 0.7661668 0.26216671 0.6694043 0.66462428 0.2177653
[5,] 0.5604505 0.04371932 0.7873665 0.44849293 0.1700327
> a[,order(x)]
abc abc col col def
[1,] 0.65855865 0.07781167 0.9815985 0.3228944 0.9982046
[2,] 0.19195563 0.80489513 0.5970836 0.9190933 0.9082061
[3,] 0.13499074 0.41154237 0.8147790 0.6487952 0.9431437
[4,] 0.26216671 0.66462428 0.7661668 0.2177653 0.6694043
[5,] 0.04371932 0.44849293 0.5604505 0.1700327 0.7873665
> order(x)
[1] 2 4 1 5 3
On Fri, 2007-08-03 at 05:36 -0700, carol white wrote:
> Hello,
> How to sort a matrix based on its column names and preserving the
identical column names.
>
> when I use mat [, sort(colnames(mat))], sort changes all column
names to unique ones. for ex, if the name of 2 columns is col, the
2nd will be changed to col.1 whereas I want to keep the col name for
the two columns
>
> col col -> col col.1
>
> thanks
>
>
> ---------------------------------
> Park yourself in front of a world of choices in alternative
vehicles.
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Dr. Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, England *
+44-1223-494466
0
Entering edit mode
Hi,
I think that there is some confusion here. First sort does not
change
any values, it sorts. The changing of column and/or row names is "a
feature", that comes with the [ operator. Details are given on the
man
page for [.data.frame.
I do not believe that there is any such behavior (currently) for
matrices. And I could not replicate the behavior described by Carol
except with data.frames, which is the documented (if peculiar)
behavior.
best wishes
Robert
m=matrix(rnorm(25), nc=5)
colnames(m) = rep("A", 5)
m[,2]
m[1,]
m[,sort(colnames(m))]
but,
y = data.frame(m)
y
#changes the colnames
y = data.frame(m, check.names=FALSE)
# but then do change the names
y[1,]
y[,sort(colnames(y))]
Oleg Sklyar wrote:
> mat[, order(colnames(mat))]
>
> order provides indexes of sorted elements without affecting their
names.
> Sort works in your case half ways only because you are sorting
> characters, and columns can be identified by characters, otherwise
it is
> wrong.
>
> Here is the working example:
>
>> x<-c("col","abc","def","abc","col")
>> a<-matrix(runif(25),ncol=5,nrow=5)
>> colnames(a) <- x
>> a
> col abc def abc col
> [1,] 0.9815985 0.65855865 0.9982046 0.07781167 0.3228944
> [2,] 0.5970836 0.19195563 0.9082061 0.80489513 0.9190933
> [3,] 0.8147790 0.13499074 0.9431437 0.41154237 0.6487952
> [4,] 0.7661668 0.26216671 0.6694043 0.66462428 0.2177653
> [5,] 0.5604505 0.04371932 0.7873665 0.44849293 0.1700327
>> a[,order(x)]
> abc abc col col def
> [1,] 0.65855865 0.07781167 0.9815985 0.3228944 0.9982046
> [2,] 0.19195563 0.80489513 0.5970836 0.9190933 0.9082061
> [3,] 0.13499074 0.41154237 0.8147790 0.6487952 0.9431437
> [4,] 0.26216671 0.66462428 0.7661668 0.2177653 0.6694043
> [5,] 0.04371932 0.44849293 0.5604505 0.1700327 0.7873665
>
>> order(x)
> [1] 2 4 1 5 3
>
> On Fri, 2007-08-03 at 05:36 -0700, carol white wrote:
>> Hello,
>> How to sort a matrix based on its column names and preserving the
identical column names.
>>
>> when I use mat [, sort(colnames(mat))], sort changes all column
names to unique ones. for ex, if the name of 2 columns is col, the
2nd will be changed to col.1 whereas I want to keep the col name for
the two columns
>>
>> col col -> col col.1
>>
>> thanks
>>
>>
>> ---------------------------------
>> Park yourself in front of a world of choices in alternative
vehicles.
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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• link
17.3 years ago
rgentleman
★
5.5k
0
Entering edit mode
Yes, I know sort does not change values -- in contrast to order it
returns sorted values and not indexes, and I pointed out the correct
solution. However, what I meant by working hal-ways is, colnames()
results in a character vector and sort rearranges elements in this
vector. matrix allows to access columns by names and thus rearranging
elements and using sort in this case should be similar (but is wrong
if
names not unique as example shows) to using order and accessing
columns
by indexes. In this case if any other values and not the colnames was
used with sort (say values in the first row), it would result in total
mess as sorted would be the values that do not identify columns:
R version 2.6.0 Under development (unstable) (2007-07-30 r42359)
> a<-matrix(runif(16),4,4)
> colnames(a)<-c("c","b","a","c")
> a[,colnames(a)] ## correct if unique names, here wrong
c b a c
[1,] 0.6674110 0.1693423 0.5741207 0.6674110
[2,] 0.4479471 0.1374272 0.1149747 0.4479471
[3,] 0.4328296 0.4990545 0.2777478 0.4328296
[4,] 0.8944030 0.1354652 0.4950811 0.8944030
> a[,sort(colnames(a))] ## correct if unique names
a b c c
[1,] 0.5741207 0.1693423 0.6674110 0.6674110
[2,] 0.1149747 0.1374272 0.4479471 0.4479471
[3,] 0.2777478 0.4990545 0.4328296 0.4328296
[4,] 0.4950811 0.1354652 0.8944030 0.8944030
> a[,order(colnames(a))] ## correct
a b c c
[1,] 0.5741207 0.1693423 0.6674110 0.43714271
[2,] 0.1149747 0.1374272 0.4479471 0.79047094
[3,] 0.2777478 0.4990545 0.4328296 0.02128344
[4,] 0.4950811 0.1354652 0.8944030 0.93321638
>
On Fri, 2007-08-03 at 09:05 -0700, Robert Gentleman wrote:
> Hi,
> I think that there is some confusion here. First sort does not
change
> any values, it sorts. The changing of column and/or row names is "a
> feature", that comes with the [ operator. Details are given on the
man
> page for [.data.frame.
>
> I do not believe that there is any such behavior (currently) for
> matrices. And I could not replicate the behavior described by Carol
> except with data.frames, which is the documented (if peculiar)
behavior.
>
>
> best wishes
> Robert
>
> m=matrix(rnorm(25), nc=5)
> colnames(m) = rep("A", 5)
> m[,2]
> m[1,]
> m[,sort(colnames(m))]
>
> but,
> y = data.frame(m)
> y
> #changes the colnames
> y = data.frame(m, check.names=FALSE)
>
> # but then do change the names
> y[1,]
> y[,sort(colnames(y))]
>
>
>
> Oleg Sklyar wrote:
> > mat[, order(colnames(mat))]
> >
> > order provides indexes of sorted elements without affecting their
names.
> > Sort works in your case half ways only because you are sorting
> > characters, and columns can be identified by characters, otherwise
it is
> > wrong.
> >
> > Here is the working example:
> >
> >> x<-c("col","abc","def","abc","col")
> >> a<-matrix(runif(25),ncol=5,nrow=5)
> >> colnames(a) <- x
> >> a
> > col abc def abc col
> > [1,] 0.9815985 0.65855865 0.9982046 0.07781167 0.3228944
> > [2,] 0.5970836 0.19195563 0.9082061 0.80489513 0.9190933
> > [3,] 0.8147790 0.13499074 0.9431437 0.41154237 0.6487952
> > [4,] 0.7661668 0.26216671 0.6694043 0.66462428 0.2177653
> > [5,] 0.5604505 0.04371932 0.7873665 0.44849293 0.1700327
> >> a[,order(x)]
> > abc abc col col def
> > [1,] 0.65855865 0.07781167 0.9815985 0.3228944 0.9982046
> > [2,] 0.19195563 0.80489513 0.5970836 0.9190933 0.9082061
> > [3,] 0.13499074 0.41154237 0.8147790 0.6487952 0.9431437
> > [4,] 0.26216671 0.66462428 0.7661668 0.2177653 0.6694043
> > [5,] 0.04371932 0.44849293 0.5604505 0.1700327 0.7873665
> >
> >> order(x)
> > [1] 2 4 1 5 3
> >
> > On Fri, 2007-08-03 at 05:36 -0700, carol white wrote:
> >> Hello,
> >> How to sort a matrix based on its column names and preserving the
identical column names.
> >>
> >> when I use mat [, sort(colnames(mat))], sort changes all column
names to unique ones. for ex, if the name of 2 columns is col, the
2nd will be changed to col.1 whereas I want to keep the col name for
the two columns
> >>
> >> col col -> col col.1
> >>
> >> thanks
> >>
> >>
> >> ---------------------------------
> >> Park yourself in front of a world of choices in alternative
vehicles.
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
Dr. Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, England *
+44-1223-494466
ADD REPLY
• link
17.3 years ago
Oleg Sklyar
▴
260
0
Entering edit mode
Oosting, J. PATH
▴
550
@oosting-j-path-412
Last seen 10.2 years ago
mat<-mat[,order(colnames(mat))]
Jan
> How to sort a matrix based on its column names and preserving the
> identical column names.
>
> when I use mat [, sort(colnames(mat))], sort changes all column
names
to
> unique ones. for ex, if the name of 2 columns is col, the 2nd will
be
> changed to col.1 whereas I want to keep the col name for the two
columns
>
> col col -> col col.1
0
Entering edit mode
alex lam RI
▴
310
@alex-lam-ri-1491
Last seen 10.2 years ago
How about this:
> m<-matrix(runif(30), nr=3)
> colnames(m)<-rep(c("A","B","C","D","E"), 2)
> m
A B C D E A
B
[1,] 0.6603121 0.7788057 0.2465374 0.8624474 0.2542933 0.1170260
0.0810228
[2,] 0.1191780 0.9388283 0.8776471 0.3523432 0.6149786 0.7219005
0.4743703
[3,] 0.3370735 0.6049742 0.9344462 0.7492387 0.2487072 0.5296768
0.7859081
C D E
[1,] 0.5279424 0.30166929 0.69852792
[2,] 0.6352592 0.65057813 0.68920975
[3,] 0.6962578 0.06894764 0.02685270
> m[, order(colnames(m))]
A A B B C C
D
[1,] 0.6603121 0.1170260 0.7788057 0.0810228 0.2465374 0.5279424
0.8624474
[2,] 0.1191780 0.7219005 0.9388283 0.4743703 0.8776471 0.6352592
0.3523432
[3,] 0.3370735 0.5296768 0.6049742 0.7859081 0.9344462 0.6962578
0.7492387
D E E
[1,] 0.30166929 0.2542933 0.69852792
[2,] 0.65057813 0.6149786 0.68920975
[3,] 0.06894764 0.2487072 0.02685270
Cheers,
Alex
------------------------------------
Alex Lam
Roslin Institute (Edinburgh)
Roslin
Midlothian EH25 9PS
Great Britain
Phone +44 131 5274471
Web http://www.roslin.ac.uk
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Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
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-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of carol
white
Sent: 03 August 2007 13:36
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] How to sort a matrix based on its column names
andpreserving the identical column names
Hello,
How to sort a matrix based on its column names and preserving the
identical column names.
when I use mat [, sort(colnames(mat))], sort changes all column names
to
unique ones. for ex, if the name of 2 columns is col, the 2nd will be
changed to col.1 whereas I want to keep the col name for the two
columns
col col -> col col.1
thanks
---------------------------------
Park yourself in front of a world of choices in alternative vehicles.
[[alternative HTML version deleted]]
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Bioconductor at stat.math.ethz.ch
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